Changes in src/Fragmentation/Exporters/ExportGraph.cpp [a2a2f7:98a293b]

File:

• src/Fragmentation/Exporters/ExportGraph.cpp (modified) (3 diffs)

src/Fragmentation/Exporters/ExportGraph.cpp

@@ -58 +58 @@
   const Graph &_graph,
   const enum HydrogenTreatment _treatment,
-  const enum HydrogenSaturation _saturation) :
+  const enum HydrogenSaturation _saturation,
+  const SaturatedFragment::GlobalSaturationPositions_t &_globalsaturationpositions) :
   TotalGraph(_graph),
   BondFragments(World::getPointer()),
   treatment(_treatment),
   saturation(_saturation),
+  globalsaturationpositions(_globalsaturationpositions),
   CurrentKeySet(TotalGraph.begin())
 {
@@ -115 +117 @@
           hydrogens,
           treatment,
-          saturation)
+          saturation,
+          globalsaturationpositions)
   );
   // and return
@@ -137 +140 @@
 }
 
-/** Internal helper to create from each keyset a molecule
- *
- */
-void ExportGraph::prepareMolecule()
-{
-  size_t count = 0;
-  for(Graph::const_iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
-    KeySet test = (*runner).first;
-    LOG(2, "DEBUG: Fragment No." << (*runner).second.first << " with TEFactor "
-        << (*runner).second.second << ".");
-    BondFragments.insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
-    ++count;
-  }
-  LOG(1, "INFO: " << count << "/" << BondFragments.ListOfMolecules.size()
-      << " fragments generated from the keysets.");
-}
-
-/** Stores a fragment from \a KeySet into \a molecule.
- * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
- * molecule and adds missing hydrogen where bonds were cut.
- * \param &Leaflet pointer to KeySet structure
- * \param IsAngstroem whether we have Ansgtroem or bohrradius
- * \return pointer to constructed molecule
- */
-molecule * ExportGraph::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
-{
-  Info info(__func__);
-  ListOfLocalAtoms_t SonList;
-  molecule *Leaf = World::getInstance().createMolecule();
-
-  StoreFragmentFromKeySet_Init(Leaf, Leaflet, SonList);
-  // create the bonds between all: Make it an induced subgraph and add hydrogen
-//  LOG(2, "Creating bonds from father graph (i.e. induced subgraph creation).");
-  CreateInducedSubgraphOfFragment(Leaf, SonList, IsAngstroem);
-
-  //Leaflet->Leaf->ScanForPeriodicCorrection(out);
-  return Leaf;
-}
-
-/** Initializes some value for putting fragment of \a *mol into \a *Leaf.
- * \param *Leaf fragment molecule
- * \param &Leaflet pointer to KeySet structure
- * \param SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
- * \return number of atoms in fragment
- */
-int ExportGraph::StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
-{
-  atom *FatherOfRunner = NULL;
-
-  // first create the minimal set of atoms from the KeySet
-  World &world = World::getInstance();
-  int size = 0;
-  for(KeySet::const_iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
-    FatherOfRunner = world.getAtom(AtomById(*runner));  // find the id
-    SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
-    size++;
-  }
-  return size;
-}
-
-/** Creates an induced subgraph out of a fragmental key set, adding bonds and hydrogens (if treated specially).
- * \param *Leaf fragment molecule
- * \param IsAngstroem whether we have Ansgtroem or bohrradius
- * \param SonList list which atom of \a *Leaf is another atom's son
- */
-void ExportGraph::CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
-{
-  bool LonelyFlag = false;
-  atom *OtherFather = NULL;
-  atom *FatherOfRunner = NULL;
-
-  // we increment the iter just before skipping the hydrogen
-  // as we use AddBond, we cannot have a const_iterator here
-  for (molecule::iterator iter = Leaf->begin(); iter != Leaf->end();) {
-    LonelyFlag = true;
-    FatherOfRunner = (*iter)->father;
-    ASSERT(FatherOfRunner,"Atom without father found");
-    if (SonList.find(FatherOfRunner->getNr()) != SonList.end())  {  // check if this, our father, is present in list
-      // create all bonds
-      const BondList& ListOfBonds = FatherOfRunner->getListOfBonds();
-      for (BondList::const_iterator BondRunner = ListOfBonds.begin();
-          BondRunner != ListOfBonds.end();
-          ++BondRunner) {
-        OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
-        if (SonList.find(OtherFather->getNr()) != SonList.end()) {
-//          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
-//              << " is bound to " << *OtherFather << ", whose son is "
-//              << *SonList[OtherFather->getNr()] << ".");
-          if (OtherFather->getNr() > FatherOfRunner->getNr()) { // add bond (Nr check is for adding only one of both variants: ab, ba)
-            std::stringstream output;
-//            output << "ACCEPT: Adding Bond: "
-            output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->getDegree());
-//            LOG(3, output.str());
-            //NumBonds[(*iter)->getNr()]++;
-          } else {
-//            LOG(3, "REJECY: Not adding bond, labels in wrong order.");
-          }
-          LonelyFlag = false;
-        } else {
-//          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
-//              << " is bound to " << *OtherFather << ", who has no son in this fragment molecule.");
-          if (saturation == DoSaturate) {
-//          LOG(3, "ACCEPT: Adding Hydrogen to " << (*iter)->Name << " and a bond in between.");
-            if (!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
-              exit(1);
-          } else if ((treatment == ExcludeHydrogen) && (OtherFather->getElementNo() == (atomicNumber_t)1)) {
-            // just copy the atom if it's a hydrogen
-            atom * const OtherWalker = Leaf->AddCopyAtom(OtherFather);
-            Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
-          }
-          //NumBonds[(*iter)->getNr()] += Binder->getDegree();
-        }
-      }
-    } else {
-      ELOG(1, "Son " << (*iter)->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->getNr()] << "!");
-    }
-    if ((LonelyFlag) && (Leaf->getAtomCount() > 1)) {
-      LOG(0, **iter << "has got bonds only to hydrogens!");
-    }
-    ++iter;
-    if (saturation == DoSaturate) {
-      while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
-        iter++;
-      }
-    }
-  }
-}
+///** Internal helper to create from each keyset a molecule
+// *
+// */
+//void ExportGraph::prepareMolecule()
+//{
+//  size_t count = 0;
+//  for(Graph::const_iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
+//    KeySet test = (*runner).first;
+//    LOG(2, "DEBUG: Fragment No." << (*runner).second.first << " with TEFactor "
+//        << (*runner).second.second << ".");
+//    BondFragments.insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
+//    ++count;
+//  }
+//  LOG(1, "INFO: " << count << "/" << BondFragments.ListOfMolecules.size()
+//      << " fragments generated from the keysets.");
+//}
+//
+///** Stores a fragment from \a KeySet into \a molecule.
+// * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
+// * molecule and adds missing hydrogen where bonds were cut.
+// * \param &Leaflet pointer to KeySet structure
+// * \param IsAngstroem whether we have Ansgtroem or bohrradius
+// * \return pointer to constructed molecule
+// */
+//molecule * ExportGraph::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
+//{
+//  Info info(__func__);
+//  ListOfLocalAtoms_t SonList;
+//  molecule *Leaf = World::getInstance().createMolecule();
+//
+//  StoreFragmentFromKeySet_Init(Leaf, Leaflet, SonList);
+//  // create the bonds between all: Make it an induced subgraph and add hydrogen
+////  LOG(2, "Creating bonds from father graph (i.e. induced subgraph creation).");
+//  CreateInducedSubgraphOfFragment(Leaf, SonList, IsAngstroem);
+//
+//  //Leaflet->Leaf->ScanForPeriodicCorrection(out);
+//  return Leaf;
+//}
+//
+///** Initializes some value for putting fragment of \a *mol into \a *Leaf.
+// * \param *Leaf fragment molecule
+// * \param &Leaflet pointer to KeySet structure
+// * \param SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
+// * \return number of atoms in fragment
+// */
+//int ExportGraph::StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
+//{
+//  atom *FatherOfRunner = NULL;
+//
+//  // first create the minimal set of atoms from the KeySet
+//  World &world = World::getInstance();
+//  int size = 0;
+//  for(KeySet::const_iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
+//    FatherOfRunner = world.getAtom(AtomById(*runner));  // find the id
+//    SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
+//    size++;
+//  }
+//  return size;
+//}
+//
+///** Creates an induced subgraph out of a fragmental key set, adding bonds and hydrogens (if treated specially).
+// * \param *Leaf fragment molecule
+// * \param IsAngstroem whether we have Ansgtroem or bohrradius
+// * \param SonList list which atom of \a *Leaf is another atom's son
+// */
+//void ExportGraph::CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
+//{
+//  bool LonelyFlag = false;
+//  atom *OtherFather = NULL;
+//  atom *FatherOfRunner = NULL;
+//
+//  // we increment the iter just before skipping the hydrogen
+//  // as we use AddBond, we cannot have a const_iterator here
+//  for (molecule::iterator iter = Leaf->begin(); iter != Leaf->end();) {
+//    LonelyFlag = true;
+//    FatherOfRunner = (*iter)->father;
+//    ASSERT(FatherOfRunner,"Atom without father found");
+//    if (SonList.find(FatherOfRunner->getNr()) != SonList.end())  {  // check if this, our father, is present in list
+//      // create all bonds
+//      const BondList& ListOfBonds = FatherOfRunner->getListOfBonds();
+//      for (BondList::const_iterator BondRunner = ListOfBonds.begin();
+//          BondRunner != ListOfBonds.end();
+//          ++BondRunner) {
+//        OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
+//        if (SonList.find(OtherFather->getNr()) != SonList.end()) {
+////          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
+////              << " is bound to " << *OtherFather << ", whose son is "
+////              << *SonList[OtherFather->getNr()] << ".");
+//          if (OtherFather->getNr() > FatherOfRunner->getNr()) { // add bond (Nr check is for adding only one of both variants: ab, ba)
+//            std::stringstream output;
+////            output << "ACCEPT: Adding Bond: "
+//            output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->getDegree());
+////            LOG(3, output.str());
+//            //NumBonds[(*iter)->getNr()]++;
+//          } else {
+////            LOG(3, "REJECY: Not adding bond, labels in wrong order.");
+//          }
+//          LonelyFlag = false;
+//        } else {
+////          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
+////              << " is bound to " << *OtherFather << ", who has no son in this fragment molecule.");
+//          if (saturation == DoSaturate) {
+////          LOG(3, "ACCEPT: Adding Hydrogen to " << (*iter)->Name << " and a bond in between.");
+//            if (!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
+//              exit(1);
+//          } else if ((treatment == ExcludeHydrogen) && (OtherFather->getElementNo() == (atomicNumber_t)1)) {
+//            // just copy the atom if it's a hydrogen
+//            atom * const OtherWalker = Leaf->AddCopyAtom(OtherFather);
+//            Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->getDegree());
+//          }
+//          //NumBonds[(*iter)->getNr()] += Binder->getDegree();
+//        }
+//      }
+//    } else {
+//      ELOG(1, "Son " << (*iter)->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->getNr()] << "!");
+//    }
+//    if ((LonelyFlag) && (Leaf->getAtomCount() > 1)) {
+//      LOG(0, **iter << "has got bonds only to hydrogens!");
+//    }
+//    ++iter;
+//    if (saturation == DoSaturate) {
+//      while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
+//        iter++;
+//      }
+//    }
+//  }
+//}